update lphy doc 1.5.0 #426

docs/index.md

@@ -77,6 +77,7 @@ Taxa & alignment
 - [selectSites](taxa-alignment/selectSites.md)
 - [species](taxa-alignment/species.md)
 - [variableSites](taxa-alignment/variableSites.md)
+- [fasta](taxa-alignment/fasta.md)
 
 Substitution and site models
 ----------------------------
@@ -153,6 +154,7 @@ Types
 - [Taxa](types/Taxa.md)
 - [Alignment](types/Alignment.md)
 - [ContinuousCharacterData](types/ContinuousCharacterData.md)
+- [FastaAlignment](types/FastaAlignment.md)
 - [MetaDataAlignment](types/MetaDataAlignment.md)
 - [SimpleAlignment](types/SimpleAlignment.md)
 - [SiteModel](types/SiteModel.md)

docs/taxa-alignment/fasta.md

@@ -0,0 +1,22 @@
+fasta function
+==============
+fasta([Alignment](../types/Alignment.md) **alignment**)
+-------------------------------------------------------
+
+A function that parses an alignment from a fasta file.
+
+### Parameters
+
+- [Alignment](../types/Alignment.md) **alignment** - the lphy alignment that is written into the fasta file.
+
+### Return type
+
+[FastaAlignment](../types/FastaAlignment.md)
+
+
+### Examples
+
+- covidDPG.lphy
+
+
+

docs/types/FastaAlignment.md

@@ -0,0 +1,30 @@
+FastaAlignment
+--------------
+### Methods
+
+- **ages**
+  - gets the ages of these taxa as an array of doubles.
+- **canonicalStateCount**
+  - the number of canonical states excluding ambiguous states in the alignment.
+- **canonicalStates**
+  - the canonical states excluding ambiguous states.
+- **dataType**
+  - get the data type of this alignment.
+- **getTaxaNames**
+  - The names of the taxa.
+- **length**
+  - gets the number of taxa.
+- **nchar**
+  - The number of characters/sites.
+- **nodeCount**
+  - the total number of nodes (left + internal) in a binary tree with these taxa.
+- **species**
+  - gets the species of these taxa as an array of strings.
+- **stateCount**
+  - the number of possible states including ambiguous states in the alignment.
+- **states**
+  - the possible states including ambiguous states.
+- **taxa**
+  - the taxa of the alignment.
+- **taxaNames**
+  - The names of the taxa.